Crystal structures of di-μ-chlorido-bis({(E)-5-(ethylamino)-4-methyl-2-[(pyridin-2-yl)diazenyl]phenolato}copper(II)) and chloridobis(1,10-phenanthroline)copper(II) chloride tetrahydrate

(E)-5-(Ethylamino)-4-methyl-2-[(pyridin-2-yl)diazenyl]phenol forms a centrosymmetric dimeric CuII complex with a double apical-basal chlorido bridge between square-pyramidal Cu centers, while 1,10-phenanthroline forms a monomeric trigonal–bipyramidal cation with equatorial Cl ligand.

The dark-red title complex crystallized from an equimolar methanol solution of (E)-5-(ethylamino)-4-methyl-2-[(pyridin-2-yl)diazenyl]phenol and CuCl 2 (phen) (phen = 1,10-phenanthroline) as a centrosymmetric dimer, [CuCl(C 14 H 15 N 4 O)] 2 . The Cu atoms are bridged by two Cl ligands and have a slightly distorted squarepyramidal coordination, where two N atoms from the azo and the pyridine moieties, a phenolic O and a Cl atom comprise the base and the other Cl occupies the apex position. The apical Cu-Cl bond, 2.6192 (4) Å , is longer than the basal one, 2.2985 (3) Å , due to Jahn-Teller distortion. The dimers are associated via weak intermolecular hydrogen bonds andstacking interactions between phenyl and pyridine rings. A monomeric by-product of the same reaction, [CuCl(phen) 2 ]ClÁ4H 2 O, has a trigonal-bipyramidal coordination of Cu with equatorial Cl ligand, and extensive outer-sphere disorder. In the structure of 4, the packing of cations leaves continuous channels containing disordered Cl À anions and solvent molecules. The identity of the solvent (water or a water/methanol mixture) was not certain. The disordered anion/solvent regions comprise 28% of the unit-cell volume. The disorder was approximated by five partly occupied positions of the Cl À anion and ten positions of O atoms with a total occupancy of 3, giving a total of 48 electrons per asymmetric unit, in agreement with the integral electron density of 47.8 electrons in the disordered region, as was estimated using the BYPASS-type solvent-masking program [van der Sluis & Spek (1990). Acta Cryst. A46, 194-201].

Chemical context
The (E)-5-(ethylamino)-4-methyl-2-[(pyridin-2-yl)diazenyl]phenol ligand (1) was synthesized from a coupling reaction of pyridine-2-diazotate and 3-ethylamino-p-cresol as a model for the lysine tyrosylquinone (LTQ) cofactor ( Fig. 1) of lysyl oxidase-like 2 (LOXL2) that is inhibited by 2-hydrazinopyridine (2HP). LOXL2 is a member of the lysyl oxidase family of proteins, and its upregulation has been closely associated with fibrosis and tumor metastasis (Moon et al. 2014;Mahjour et al., 2019;Wei et al., 2021). We have recently identified 2HP-modified LTQ, LTQ-2HP ( Fig. 1) in 2HPinhibited LOXL2 by mass spectrometry-based peptide mapping (Meier, Go et al., 2022). Since there is no structural information of a catalytically competent form of LOXL2, we conducted comparative spectroscopic studies of 2HP-inhibited LOXL2 and the corresponding model compound in solution, in order to understand the spatial arrangement of the LTQ cofactor and the active site Cu II . The UV-vis spectroscopic feature of 2HP-inhibited LOXL2 indicated the ligation of LTQ-2HP to the active site Cu II (Fig. 2).
In order to model the LTQ-2HP ligated to the active site Cu II , 1 was mixed with an equimolar amount of dichloro-(phen)Cu (phen = 1,10-phenanthroline) in anhydrous methanol to isolate dark-red solids (2), where the phen ligand was used to mimic two of the three His ligands of the active site Cu II in LOXL2 (Meier, Kuczera et al., 2022). Upon slow evaporation of methanol solution of 2, dark-red crystals (3) were isolated and characterized as a dimeric complex [CuCl(C 14 H 15 N 4 O)] 2 ( Fig. 1).
After isolation of 3, green prismatic crystals (4) were isolated from the mother liquor and identified as a monomeric complex, [CuCl(phen) 2 ] À Cl + Á4H 2 O (Fig. 1). Herein we report the crystal structures of 3 and 4.

Structural commentary
The molecule of 3 (Fig. 2) has a crystallographic inversion center. Each Cu atom is penta-coordinated by N1, N3, and the deprotonated O1 of the oxoanion 1, as well as two inversionrelated bridging chloride ligands, Cl and Cl'. Atoms N1, N3, O1 and Cl are nearly coplanar and comprise the base of a distorted square pyramid while Cl' occupies the apical position. The apical Cu-Cl bond is ca 0.32 Å longer than the basal one due to the Jahn-Teller effect (Addison et al., 1984). The Addison parameter, = ( -)/60 = 0.007 (where = 160.67 and = 161.00 are the widest bond angles) indicates a small distortion from an ideal square-pyramidal geometry ( = 0) towards a trigonal-bipyramidal geometry ( = 1). The coordination polyhedra of the two Cu atoms share one baseto-apex edge (Fig. 1b)  (a) The covalent modification of the LTQ cofactor of LOXL2 by 2HP. After the tautomerization of the hydrazone to the azo form, LTQ-2HP ligates to the active site Cu 2+ . The 2HP-modified LTQ (LTQ-2HP) containing the peptide was detected by mass spectrometry (Meier, Go, et al., 2022). Based on the close resemblances of UV-vis and resonance Raman spectra of 2HP-inhibited LOXL2 and the model compound 2, we hypothesize that LTQ-2HP serves as a tridentate ligand to the active site Cu II in LOXL2 . The +2 charge of Cu II is expected to be canceled out by the 4-oxoanion of LTQ-2HP and a nearby acidic residue or a water molecule (Meier, Kuczera et al., 2022). (b) During the recrystallization of the dark red solids (2) isolated from an equimolar mixture of the LTQ-2HP model compound (1) and CuCl 2 (phen) in anhydrous methanol, we first isolated dark-red crystals (3), then also isolated (4) from the mother liquor that was left for a week at room temperature. parallel to each other (with an interplanar separation of 1.789 Å ), in a type II arrangement as classified by Rodriguez et al. (1999). The Cu 2 Cl 2 plane is perpendicular to the basal planes. The geometry agrees with that in other Cu 2 (-Cl) 2 centers (Sasmal et al., 2013;Rodriguez et al., 1999). In the ligand 1, the aromatic phenyl and pyridine rings are conjugated through the N N (azo) bond of 1.301 (2) Å and adopt a E, or trans, configuration about this bond, with a C-N N-C torsion angle of À179.0 (1) . The dimer also contains two pairs of weak intramolecular hydrogen bonds, C11-H11Á Á ÁCl and C11-H11Á Á ÁO1 (Table 1).

Figure 3
The cation and ordered water molecule in the structure of 4. Atomic displacement ellipsoids are drawn at the 50% probability level.

Supramolecular features
The crystal packing of 3 is shown in Fig. 4. Each molecule forms ten weak intermolecular hydrogen bonds C-HÁ Á ÁX, where X = Cl or O (Grabowski, 2021). The Cl atom is engaged in four such interactions and the O atom in two (supporting Fig. 1A). Additional stabilization is provided by off-center parallelstacking interactions (Janiak, 2000;Martinez & Iverson, 2012) between two phenyl rings, between two pyridine rings, or between a phenyl and a pyridine ring ( Fig. 4 and supporting Fig. 1B,C). The distances between ring centers (centroid-centroid distances), the distances between the ring center and the plane of the ring (plane-plane distances) and the angle between the ring normal and the center of the opposite ring of the three modes ofinteractions are summarized in Table 2. Remarkably, the amino-H atom is not engaged in any hydrogen bond, probably due to screening by two adjacent methyl groups.
In the structure of 4 (supplemental Fig. 2), the packing of cations leaves continuous channels containing disordered Cl À anions and solvent molecules. Of the latter, one water molecule per asymmetric unit is ordered, being 'anchored' by an O1-H1AÁ Á ÁCl1 hydrogen bond with the cation [O1Á Á ÁCl1 = 3.173 (3), H1AÁ Á ÁCl1 = 2.34 Å ]. The rest of the solvent is intensely disordered and its identity (water or a water/ methanol mixture) was not certain. The disordered anion/ solvent regions comprise 28% of the unit-cell volume. The disorder was approximated by five partly occupied positions of the Cl À anion and ten positions of O atoms with a total occupancy of 3 -presumably water molecules whose hydrogen atoms could not be located. This gives a total of 48 electrons per asymmetric unit, in agreement with the integral electron density of 47.8 electrons in the disordered region, as was estimated using the BYPASS-type solvent-masking program (van der Sluis & Spek, 1990) on the OLEX2 platform (Dolomanov et al., 2009).

Database survey
Several crystal structures of penta-coordinated centrosymmetric Cu II dimers with the Cu atoms bridged by two Cl ligands and bonded to ligands with N and O atoms, have been deposited in the Cambridge Structural Database (CSD, Version 5.38; Groom et al., 2016), viz. FEWFAO (Rodriguez et al., 1999, MUNWIB, MUNWOH (Kapoor et al., 2002), YECGUK (Das et al., 2012), SIDQED (Sasmal et al., 2013), and POJKOQ (Smolentsev et al., 2014). However, no complexes with ligand 1 were found. To our knowledge, 3 is the first example of a penta-coordinated centrosymmetric Cu II dimer in which the Cu atoms are bridged by two Cl ligands and are bonded each to two N atoms (pyridine N and aromatic -N N-) and a phenoxy-O atom. There are multiple structures of phen and its derivatives complexed with Cu II , the two structures closely related to 4 being PENCUN (Anderson, 1975) and XUMZOU (Yamada et al., 2002), see Section 2. Crystal packing of 3 (a), showing intermolecular hydrogen bonds (b) and phenyl-phenylstacking interactions (c) ( is the angle between the ring normal and centroid-centroid vector, d is the displacement between the rings). Table 2 Distances and angle (Å , ) of intermolecularinteractions in 3.

Crystallization
Compound 1 was purified by recrystallization from methanol by slow evaporation. Dark-yellow needle-like crystals of 1 were obtained after a week at room temperature. CuCl 2 (phen) (123 mg, 0.39 mmol) was added to a suspension of 1 (100 mg, 0.39 mmol) in 5 ml of methanol. The reaction mixture was sonicated to completely dissolve solids and subjected to slow evaporation of methanol at room temperature. Dark-red single crystals of 3, suitable for X-ray crystallography, were obtained within a day. After removing the crystals of 3, small green crystals of 4 were formed from the mother liquor. Recrystallization of 3 by slow evaporation of an equimolar mixture of 1 in methanol and CuCl 2 in a minimal amount of water at room temperature gave dark-red crystals within a couple of days (Fig. 1). The UV-vis spectra of crystalline 3 obtained by two methods are identical and superimposable to the visible region of the UV-vis spectrum of 2HP-inhibited LOXL2 (Fig. 5). These results strongly support our hypothesis that 2HP-inhibited LOXL2 contains LTQ-2HP that is ligated to the active site Cu 2+

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. In 3, all H atoms were refined in isotropic approximation. In 4, the H atoms of the disordered water molecules were ignored, H1A was refined in an isotropic approximation, other H atoms were placed in idealized positions (C-H = 0.95, O-H = 0.84 Å ) and refined as riding on their carrier atoms with U iso (H) = 1.2U eq (C) or 1.5U eq (O). The treatment of the disorder is described in the Supramolecular features section.  UV-vis spectra of 2HP-inhibited LOXL2 (LOXL2-2HP) (in black) , crystalline 3 isolated from a 1:1 mixture of 2 with CuCl 2 (phen) (in blue), and crystalline 3 isolated from a 1:1 mixture of 2 with CuCl 2 (in red). All spectra were recorded in 50 mM HEPBS buffer (pH 8.0).  program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: Olex2 1.5 (Dolomanov et al., 2009); software used to prepare material for publication: Olex2 1.5 (Dolomanov et al., 2009).

Crystal data
[CuCl (C 12  where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max < 0.001 Δρ max = 1.06 e Å −3 Δρ min = −0.48 e Å −3 Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.